Super Mario: Koopacalypse
by MissBeiBauble
Summary: Everyone knows how the story goes. But what happens when Bowser finally manages to change the ending, throwing the Mushroom Kingdom into a new era of darkness and despair? Now that the princess can never protect her people again, the citizens must look towards their scattered heroes for aid. Can the Mario Bros save what's left of their beloved kingdom? They'll have to survive first
1. Prologue

**Super Mario: Koopacalypse**

 **By: cide301  
**

 **Editing By: MissBeiBauble  
**

 **Prologue**

Everyone knows how the story goes. One day, an evil king known as Bowser Koopa attempted to have his revenge against all the Mushroom People for banishing the Koopas into the wretched world now known as Dark Land.

So, Bowser set a curse on these Mushroom People by turning them into brick. It had seemed that the Mushroom People were helpless against Bowser's black magic.

However, there was one soul, with purifying powers, that could free her people of this horrible curse. And that would be Princess Peach Toadstool. Knowing that this would thwart his evil plot, Bowser had sent his Goombas, traitors to the Mushroom People, to kidnap the Princess. And because Bowser's Castle was surrounded by evil magic, the Princess's powers were useless.

It had seemed that Bowser and his Koopa Troop had won the day. However, there was a brave warrior from a far-off land who was strong and brave enough to forge through soaring bullets, flailing hammers, and scorching fireballs. This man, better known as a plumber, was the world-famous Mario Mario.

Mario had saved the Princess countless times, through the craziest adventures, had met new friends, and fought mortal enemies. Mario's powers were limitless, he would never give up. No matter the circumstances, he would never rest until Princess Peach was safe from the clutches of the wrathful Koopa king.

And after more than 40 years of failure to seek his vengeance, Bowser became desperate. He had cared for Princess Peach and had made a few attempts to marry her, but only now he realized that holding her captive was what was hindering his plan, that that was the true weakness of his schemes all this time. So, he had no choice…but to end Peach's game.

And that's what happened. Now that Princess Peach, the only one who could counteract against black magic, had perished, the Mushroom Kingdom was in the palm of Bowser's hand. He released a huge bomb of black magic that had detonated and turned any Toad close by into a lifeless rock.

Mario and Luigi, now knowing that there was no goal to their game anymore, packed their bags, got on their Kart, and fled Toad Town…

 **A/N: Hello, thanks for checking this out! This story is being written by my younger brother, who has given me permission to edit and post it onto my account, as he doesn't have one (this being his first fanfic, and all). Please don't forget to drop a review, he'd love to know how he can improve and what he's doing well. See you in the next chapter, and I h** **ope you guys enjoy the ride - it's a doozy for sure!**


	2. (1-1) A Fungus Among Us

**Chapter 1-1**

 **A Fungus Among Us**

"Leave no one alive!" shouted Mario's eternal rival, Wario, who was staring at the burning mushroom house with his partner in crime, Waluigi.

"Wah! Of course I know not to leave anyone alive! What do you think Lord Bowser is paying us for!?" sneered Waluigi. The two criminals searched the house without getting too close to the fire, but all they could see was shattered glass and torn bags, presumably filled with Super Mushrooms…and Toadette.

"My sister," sobbed Toad, as he watched Wario and Waluigi search the destroyed house. Toad sobbed some more, "I can't believe they actually killed my sister…"

"Yeah, they're not kidding around this time," Luigi squeaked. "I bet Bowser's paying them a whole treasure trove for every house!"

Mario glumly reminded the two, "We better get back to the kart before they spot us." The three were behind a large bush. Mario and Luigi had come to rescue Toad and Toadette before the Wario Bros. had come to dismantle the house. Unfortunately, they only made it out with one of them.

It had been 6 months since the death of the Princess. Since then, Bowser had ordered all Toads to be eliminated, as he did not even care to see them as brick. So he hired Wario and Waluigi to take care of business, for the price of a few thousand gold coins. Mario and Luigi were trying to gather as many of their friends as they could.

The Mario Bros. and Toad rushed to the kart, which was now upgraded to fit more than enough people and store as much pasta as they needed. They drove away from the mess. In the kart, Toad had been curious as to what happened to the Bros.

"Um, guys," he said, "Where were you? The entire kingdom is flooded with bad guys and you guys are thinking about running away? Come on!" he said stubbornly. "That's not the Super Mario Bros. _I_ remember. Where's the persistence? The courage and-"

But just before Toad could finish, Luigi interrupted, "There's not much rattling going on in that big head of yours, is there?"

"It's not that simple, Toad," Mario pointed out, in the most depressed tone Toad has ever heard in his life. "With the Princess gone, who's going to free all those bricked Toads?"

"Um, has anyone here forgot that my sister was _killed_!?" Toad shouted. "Bowser doesn't give a crap about us being brick or stone or whatever anymore! He just wants us dead!"

There was complete silence in the kart. Then after a long time, Mario spoke up.

"I have a plan," he said. "But first we need to find Yoshi, Daisy…" He paused for a moment. "…And Professor Gadd." Toad looked puzzled.

"Why do we need that old coot? He probably died of old age by now."

"If he isn't alive, then our plan will be a failure," Mario replied simply.

He parked his kart next to a crummy looking tent, only roomy enough for two. There were empty bowls and pizza boxes.

Back in the kart, Mario turned to Luigi and Toad. "You two will take the motorbike and head for Boo Woods. Search every inch of that lab for him. I'll stay with the kart and look for Yoshi and Daisy." Luigi, without even thinking about second guessing his order, hopped on the bike.

Toad was even more confused, "We're splitting up? Seriously can't you just explain what's going on here?!"

Mario looked at him. Then he replied, "If I told you, you'd think I was insane."

Toad just grumpily replied, "Well, _I'm_ gonna go insane if you don't tell me what you're up to!" Just then, Luigi grabbed Toad and dropped him on the back seat of the bike before driving off.


	3. (1-2) A Familiar Face Under the Sea

**Chapter 1-2**

 **A Familiar Face Under the Sea**

As Luigi and Toad drove off to find Professor E. Gadd, Mario powered up his kart again and drove off to find Daisy. Mario had to be on his guard though, because Bowser's spies where everywhere. And if they ever caught a glimpse of the shining red of his kart hood, his game was sure to end.

Mario managed to drive past all patrolling Fly Guys and Mechakoopas around Grass Land. The night was cold, but Mario was sweating with the stressing thought of being captured. And knowing Bowser, he would not let him die so easily, but rather torture him, day and night. Mario was imagining all the awful things Bowser could possibly do to him. Poisoned spaghetti? Goomba Head-Bonk Storm? CD-i GAMES!? Whatever it could be, he did not want to find out.

At last, Mario arrived at the coast of Grass Land, where a large expanse of sea was just ahead of him. Mario flipped a switch on his kart and a submarine-like propeller jolted out the end of the end of it. He drove into the water.

Mario knew it'd be a long journey to reach Sarasaland, but he also knew that Daisy was his friend, and his brother would be eternally grateful for this. So Mario pressed on, until he hit something that felt like a rock. Mario stepped out of the kart to see what it was.

"No problem. I'll just give this rock a push and then-" but just as he was beginning to move the rock, the rock spoke to him.

"Who dares call me a rock!?"

Mario had nothing to say. After all, what would you say to a rock who didn't want to admit being a rock? Mario then spoke slowly, "Um… Hello?"

Then the rock spoke again, "Yes hello, do you realize that I just had this tentacle fixed?" That's when Mario realized it wasn't a rock, but a blooper! But not just any blooper, it was…

"Gooper Blooper?"

"That's right land-freak! How would you like a tentacle sandwich!?" Gooper Blooper hissed, and it lashed its tentacles at Mario. Being an old pro at platformers, Mario jumped over the attacks flawlessly. But what he didn't expect was that the Blooper shot lasers from the tips of its tentacles. Mario had barely avoided these surprise attacks before he got a full glimpse of the blooper boss. Gooper Blooper was outfitted with all kinds of advanced tech on him. He had steel surrounding his body, and he seemed to have a few extra tentacles made with whirring saws and spinning drills. He even had a red mechanical camera replacing his right eye.

"So, Gooper ol' pal," Mario said, very friendly but with a hint of fear in his voice, "You look good, man. Cool new… Um… Metal?" Mario was very tempted to just jump in the kart and drive right around him, but Gooper Blooper's long-range attacks would destroy the kart within seconds. He had to think of a new strategy. That's when Mario remembered something from his kart. He ran back to go get it.

"What's the matter," the squid of steel mocked, "Too scared to climb out of your hiding place?" Mario then popped out over confidently.

"No, I just don't you to be so scared to finish this!" That's when Gooper Blooper shot multiple beams of lasers at the plumber, all approaching him fast. But at the last second, Mario whipped out his sparkling yellow cape, and reflected all the lasers back at the blooper. And before you knew it, Gooper Blooper's tech was dismantled, and his face was scorched with red-hot lasers. He toppled down, motionless. But Mario didn't celebrate his victory for long; he knew the Mecha-Cheeps would be out searching for him. So he got back into his kart and drove away for the mess as if nothing had happened.


	4. (1-3) The Last Letter

**Chapter 1-3**

 **The Last Letter**

After crossing the sea, Mario had arrived in Sarasaland, a world which he's only been in once. When he drove into the town though, it didn't look any better than it did in the Mushroom Kingdom. Hammer Bros. and Chain Chomps had raided the shops and burned down the houses. Mario hadn't even known that there were actual civilians until now. As he drove, he found more innocent Toads, captured, and transported to the Mushroom Kingdom. Since the black magic's range can only reach so far, Bowser's minions had to take the Toads aboard his Doom Sub and to be shipped back to the Mushroom Kingdom.

Mario wished he could help, but he knew he was outnumbered. So, he drove away, silently into the night. And that's when he found Princess Daisy's castle, now completely destroyed, with cracked shingles and broken glass. He entered in, only to find nobody inside. Not even a single Koopa Troopa.

"Hello? It's-a-me, Mario!" he called, expecting an answer. It was highly unusual for him to call that without attracting any sort of attention. The castle wasn't quite as big as Peach's Castle, so it took much shorter time to search. But not a single trace of Daisy…anywhere.

That's when Mario found a letter on the ground. It was a letter sent from Princess Peach, about 6 months ago, just before the Koopacalypse started. He remembered now. Bowser had killed Peach _after_ he built the Black Magic bomb, so when she was alive, Peach had prior knowledge of Bowser's wicked plot. So, she sent a letter to Princess Daisy. Mario picked up the letter and began reading it.

 _"_ _Dear Daisy,_

 _Something terrible is about to happen. Bowser has built some sort of bomb and it could possibly destroy us all. Please, take shelter. Find someplace to hide. But not your castle, they'll look for you there first! This could very well be the end, Daisy. I want you to know that I've always loved playing tennis and throwing parties with you. Goodbye now._

 _Princess Toadstool_

 _Peach_ _"_

Mario held the letter close to him. Peach loved writing in general, especially letters to her friends and family. It was a shame to see the content of her last letter to be about an apocalypse waiting to happen.

But that letter he read gave him a clue. He thought for a moment where Daisy could be. And that's when he got an idea.


	5. (1-4) Oh Daisy! Daisy!

**Chapter 1-4**

 **Oh Daisy! Daisy!**

Mario went into the Easton Kingdom, in hopes of finding the tower that Daisy was captured in so many years ago. Sure enough, it was still standing. Actually, it looked exactly the same at it did years ago.

"Someone must've done some cleaning, or nobody's even bothered to look here," Mario thought to himself. Either way, it meant that Daisy had to be here.

When Mario entered, it didn't take long for him to make it to the end, especially since all the traps were deactivated and the enemies had left. At last, Mario had found Princess Daisy. Surprisingly, he found she had no scratches or bandages on her like himself or Luigi, except for a few scratches and torn pieces at the bottom of her dress.

"Oh Daisy! Daisy!" Mario shouted with relief. "Thanks goodness you're okay!" Then Daisy gave him a glare that was most unsettling, especially for her.

Mario felt a bit shocked to see this, and then she spoke to him, "Yeah, why wouldn't I be. I've stayed shut up in here for like, 6 months. I thought you and Luigi were actually gonna do something instead of let the world die while you eat your pasta!"

Now Mario was offended, so he snapped back, "What do you mean? Luigi, Toad, and I have been trying to escape this apocalyptic world while scrounging around for food and shelter."

Now it was Daisy's turn to hiss, "So you're not saving the day like always? You're giving up!? What's wrong with you!?"

"Do you not see what's happening outside? It's too late, I can't stop this now!"

"So, what's your grand plan for escape? Warp Zone?" Daisy asked after a big sigh, seemingly calmed down a bit. She could see how upset Mario was and, well, Mario wasn't usually this upset. Ever. So, she went along with his plan… Whatever that might be.

"No. I can't tell you just yet. Besides, we need E. Gadd, and that's where Luigi and Toad are going to get him," Mario said, trying to change the subject.

"Oh my God!" Daisy shrieked in horror, "Luigi! Please tell me he's doing okay! And please tell me he still has his sexy mustache and not an ugly beard!" she asked as if it was a matter of life and death.

"He's fine," Mario assured, "and he still has the 'stache."

"Oh yes! Thank God!" Daisy breathed with a sigh of relief.

"If you just come with me, I can help you leave this place."

Daisy didn't want to. She was the princess of her own kingdom, it was her responsibility to keep it safe. But up to this point, she already failed that job, and now what choice does she have?

"Alright Mario," she sighed disappointingly, "Take me away…"


	6. (2-1) A Royal Meeting

**Chapter 2-1**

 **A Royal Meeting**

Just on the other side of the Mushroom Kingdom was Boo Woods, a place notorious for being one of the scariest parts of the Kingdom. Creepy trees, stinky mud, and ominous background music. But what it was best known for was its inhabitants; you guessed it, Boos.

Their ruler, King Boo, was working on some of his card tricks in an old, abandoned mansion, unaware of the rampaging Koopacalypse that was going on outside of the woods. That's when one of his Boo Servants came through the door to see him.

"Your scariness," the Boo whispered.

"What's the news?" King Boo asked as he twirled a card around.

"King Bowser wants to speak with you," the Boo Servant whispered.

King Boo groaned. Every once in a while, Bowser would come and ask him to help him deal with the Mario Bros. in hopes of succeeding in kidnapping Peach. King Boo could already tell by the numerous schemes in the past that this time, whatever the plan is, it wouldn't work.

"Fine, let him humor me for a little bit," he sighed.

The Boo Servant creaked open the door to let in Bowser and his servants. When Bowser came in, though, King Boo seemed shocked to see him. Bowser wasn't the same as before.

He had burnt marks all over his scales, probably from the countless times he's been dropped into the lava, and his shell was cracked from top to bottom. The spikes and horns on him were chipped and scratched. His entire left arm was down to nothing but bones. And his hair had grown longer, and his eyebrows were fuzzier.

King Boo was a bit startled by all this. "Why, Bowser, old chum," he said, trying not to let Bowser's appearance distract him.

Bowser came closer with his minions, Ludwig, Iggy and two Hammer Bros.

"And, what might the almighty King of Koopas be doing in Boo Woods? Another 'Princess Kidnapping Plan'?"

"No…" Bowser said, in a much deeper voice than usual, "Princess Peach's game has already ended."

King Boo almost choked on his own drool after hearing this. He knew scaring the crap out of people was one thing but to kill someone would have to be serious. Even more so, he knew how much Bowser liked Peach. He knew he shouldn't be asking how it all happened, but his curiosity got the better of him.

"Well, I'm very sorry this happened Bowser, but I- "

"I killed her. Intentionally."

"Excuse me, what?"

"Without her in the way, I can rule all the land. I have enough Black Magic to create this wretched universe in my image!"

King Boo almost didn't know what to say. Bowser wasn't usually like this.

"You seem…different…"

He tried to change the subject, "Well, what about the Mario Bros.? Those Gullible Soup Sucking Losers! It's gonna cost you a good 200 coins for me to- "

"I didn't come for your assistance," Bowser interrupted, his voice getting louder. "I came to give you a warning. I've already took over Acorn Plains through Lemmy, the Layer-Cake Desert through Morton, and now, Iggy here shall be taking over Soda Jungle. Which includes Boo Woods."

"Boo Woods!? But I already control that area!"

"I will ask you only once: leave this place, and I will spare you…"

"Never! You've tested my patience for the last time, Bower!"

King Boo called to his minions, "Boos! Attack!"

"Koopa Pack! Attack!"

As soon as Bowser said that, a huge explosion went off in the back of the mansion. Wario and Waluigi were there, and they grabbed their Light Boxes and charged towards King Boo. While Ludwig and Iggy attacked the army of boos, Wario and Waluigi were shining bright lights in King Boo's face. The Hammer Bros. made sure that none of the boos escaped the mansion, they would finish off all of them. Then, as if time itself froze, a loud shriek was heard. King Boo was fading away…

"Curse…you…Bowser…" He faintly shouted, and he faded away as if he never existed.

Bowser grinned as he watched King Boo fall. He was definitely not like his usual self. He was more ruthless, cunning, and showed no mercy for anyone.

"Alright Iggy," he said to him, "The jungle's yours."

"Bahaha!" laughed Iggy, in his own demented laughter.

Bowser was now one step closer to taking total control of the kingdom. He could not be stopped.

 **A/N: Please don't forget to leave a review! They'd mean the world to us! :)**


	7. (2-2) Within Boo Woods

**Chapter 2-2**

 **Within Boo Woods**

Luigi and Toad were making their way to E. Gadd on their bike through the creepiest part of the wood. "It's pretty clear this old coot likes his alone time…" muttered Toad as they passed some trees, which oddly looked like they were staring at them.

Luigi didn't say a word. Toad was just now realizing that Luigi should be trembling in fear and crying like a baby. This time he was not, he just drove on as if he'd been here countless times. Toad was trying not to get scared of…well, anything really. Everything here freaked him out. But then he saw something that he had to tell Luigi about.

"Mecha-Koopas!" He shouted, and instantly, Luigi drove faster. But that's when unexpectedly, a Mecha-Koopa managed to blow fire at the bike's engine. The bike exploded, and Luigi and Toad flew right out of it. They landed on the muddy ground, which was harder than it looked. All of the Mecha-Koopas were surrounding them in a circle, and Luigi and Toad stood in the middle, back to back. Then, part of the Mecha-Koopa circle opened up to make room for a tall, pointy-mustached man: Waluigi.

"Something told me you slime-balls would be here. While Master Iggy's making the preparations for his fortress, I'm stuck on patrol duty thanks to you!" Waluigi sneered.

"Where's Wario?" Toad asked. It was very unusual to see the two criminals separated.

"Wario's out taking care of business. But now I get to deal with you!" Then he turned to his Mecha Koopas. "Take the little fungus away, I want the pleasure of finishing my rival!"

"Have it your way, Waluigi!" Luigi snapped back at him.

The two began to fight, starting with Waluigi hurling Bob-Ombs at him, but Luigi had expertly dodged the attacks. Then, Waluigi grew furious and threw a huge Bob-Omb at him, but Luigi had already pulled out his mighty Poltergust 5000, still fully functional without even a scratch, and sucked up the Big Bob-Omb before shooting it right back into Waluigi's face. The blast was so big, it sent the crook into such a height he could (probably) not survive, and all the Mecha-Koopas had stopped in place.

"Run!" Cried Luigi, and he and Toad fled the scene.

As both Bros. had learned from experience, Mecha-Koopas are, indeed, explosive.

After that, the two had to go on foot. But they knew they were getting close, for they saw a familiar, green pathway, leading up to an old shack.


	8. (2-3) The Stolen Painting

**Chapter 2-3**

 **The Stolen Painting**

Luigi and Toad approached the old shack. Luigi definitely recognized the place. It was the professor's old lab. He and Toad climbed down the ladder, which had led them deep underground. It was dark in there, and very dusty too.

"Luigi, you sure this is the right place? It's awfully spooky here…"

Luigi simply replied, "Yeah, I know. E. Gadd likes to spend his time in the creepiest parts of the world."

Toad not only felt uneasy about this, but he could also sense that Luigi wasn't being his usual self. He understood the kind of circumstances that they're in, but Luigi almost looked like he wanted to say something, to get it off his chest, but he simply couldn't.

"Well, Toad?" Luigi asked. "What are you waiting for? Let's split up and search."

"S-Split up? In this Level 9 horrific laboratory? Forget it!"

Luigi was fed up with Toad's stubbornness, but just as he was about to say something, they heard a ghostly laugh, one that echoed through the clouds of dust and creaking wood on the walls. Both Luigi and Toad froze. Luigi had still not gotten over the 23 Portrait Ghosts, which were very human-like spirits that he had been forced to collect during his quest to rescue Mario.

Luigi whipped out his flashlight. And as if he couldn't walk shakingly towards the sound any slower, Toad was clinging on to Luigi's leg with his eyes shut tight.

Eventually, the pair reached E. Gadd's room, where he did most of his inventing. The laughter grew louder, but weirdly, it didn't sound like the laugh of intimidation Luigi was used to when dealing with ghosts, but it was rather happy and joyful. Toad didn't care who or what was laughing, he just wanted to get out of that lab as soon as possible.

And that's when Luigi came across a machine made up of a toaster, a miniature pipe and a couple of added nozzles. Toad had finally let go of Luigi's ankle because he spotted something very peculiar. When he realized what he saw, he almost shrieked before covering his mouth. He glanced towards Luigi, who was still examining the strange device, and pointed towards a pair of glasses. Glasses with huge, swirly lens. Luigi's face froze in shock. Those were E. Gadd's glasses. But before he had time to think of how this could've happened, the creepy laughing sounded like it was right on top of them. By pure instinct, Luigi shined his light on the ghoul's face.

"AAUUUGGHH! Criminy, that burns!"

Luigi could recognize that voice anywhere. He turned off his flashlight and saw a floating, greenish ghost. It was the ghost of Professor Elvin Gadd!

"Ho hooo! My boy, I didn't think you'd ever return! What's it been, 20 years since our Dark Moon Quest?" the Professor exclaimed with joy.

"Egad! You're a ghost!" Toad shrieked.

"Indeed, I am," he said calmly. "Now I know what you youngsters are thinking, but the fact is I didn't die. I converted my physical body into a spiritual form. Eh, unfortunately, my glasses didn't seem to make the cut. I did this so that I could live forever and continue to benefit the world with my technology!"

Luigi loved to see his old friend again, but he had to burst his bubble. "But, you do realize that we're stuck in the Koopacalypse, right? Peach is dead, and Mario's got a- "

"Oh, is this what it's all about? I was just looking through my para-scope to find King Boo being wiped out by Bowser and his goons. Now, Iggy owns this forest, along with the rest of Soda Jungle."

"If he keeps this up, Bowser will own the whole world!" Toad exclaimed.

"Come with us, Professor," Luigi spoke up. "We have a plan, but we need your help!"

"Is it something you need me to build?"

"Yeah, we need you to- "

But just as Luigi was about to finish, the three of them heard footsteps from above. They heard faint sounds of insane laughter and mechanical feet.

"Bah! Where are they?" Iggy shouted as he walked, unaware that the people he was looking for were right underneath him.

Then, the three heard the footsteps and mechanical noises go past them. They believed that they were safe.

"Phew," Toad sighed, relieved.

Then they heard something drop down to the lab. It was dark, so Luigi turned on his flashlight, revealing that a Bob-Omb was about to go off on them.

 _"_ _Eek!"_ cried Luigi, and the three ran back from it.

"This way!" yelped E. Gadd. He had led them to the Ghost Portrificationizer, an old device that could turn ghosts into paintings.

"Everyone get behind it!" yelled E. Gadd. Luigi and Toad squeezed their way behind the big machine with the circular window, and ducked and covered. The Bob-Omb had exploded, and the blast was so loud, their ears were ringing in pain. Surprisingly though, the Portrificationizer hadn't gained a scratch. With their ears in pain and smoke blocking their visual, they simply stayed ducked until Luigi got curious as to where the ghostly E. Gadd had went.

Luigi got up and peeked through the window on the back of the machine. The smoke had cleared a little. But in the fog, he could see four Boos carrying E. Gadd, who was struggling for release.

"Unhand me, ghosts!" the Professor strictly ordered. But of course, the Boos couldn't care less and continued to carry the ghoulish scientist towards the vent of the machine where the ghosts would go into to get transformed into paintings. Luigi attempted to spring into action by whipping out his Poltergust 5000, but before he could do so, Iggy had surprise attacked him and lashed out with a powerful blast of magic from his wand. Luigi fell on his back with a thud, and Toad saw how Professor E. Gadd transformed into a painting before his very eyes. Iggy grabbed the painting and marched off the lab.

"Come on boys!" he ordered towards his Boos. "Next stop! Twinsy Tropics!"


End file.
